store PsmProtein in a map with accession as key More...

#include <psmproteinmap.h>

Public Member Functions
	PsmProteinMap ()

virtual	~PsmProteinMap ()

std::pair< std::map< QString, PsmProtein >::iterator, bool >	insert (const PsmProtein &psm_protein)
	standard map insert of a PsmProtein (accession is the key)

void	writeMap (CborStreamWriter &writer) const
	writes the protein map in a cbor output stream this output a CborMap structure directly in the output stream

void	readMap (CborStreamReader &reader)
	reads the protein map from a cbor input stream

std::size_t	size () const
	get protein map size

const pappso::cbor::psm::PsmProtein &	getByAccession (const QString &accession) const
	retrieve a PsmProtein with its accession

void	merge (const PsmProteinMap &other_protein_map)
	merge with other protein map

void	reduce (const QStringList &accession_list)
	reduce to protein accessions listed in input

std::map< QString, PsmProtein > &	getProteinMap ()

Private Attributes
std::map< QString, PsmProtein >	m_proteinMap

Detailed Description

store PsmProtein in a map with accession as key

Definition at line 54 of file psmproteinmap.h.

Constructor & Destructor Documentation

◆ PsmProteinMap()

pappso::cbor::psm::PsmProteinMap::PsmProteinMap ( )

Default constructor

Definition at line 33 of file psmproteinmap.cpp.

34{

35}

◆ ~PsmProteinMap()

pappso::cbor::psm::PsmProteinMap::~PsmProteinMap ( )

virtual

Destructor

Definition at line 37 of file psmproteinmap.cpp.

38{

39}

Member Function Documentation

◆ getByAccession()

const pappso::cbor::psm::PsmProtein & pappso::cbor::psm::PsmProteinMap::getByAccession ( const QString & accession ) const

retrieve a PsmProtein with its accession

Returns: PsmProtein const reference

Definition at line 164 of file psmproteinmap.cpp.

{
  auto it = m_proteinMap.find(accession);
 
  if(it == m_proteinMap.end())
    {
      throw pappso::ExceptionNotFound(QObject::tr("%1 accession not found").arg(accession));
    }
  return it->second;
}

Referenced by pappso::cbor::psm::PsmFileReaderBase::currentProteinRefListContainsDecoy(), pappso::cbor::psm::PsmFileReaderBase::currentProteinRefListContainsTarget(), pappso::cbor::psm::CborScanMapBase::populateProteinMapUsingOldProteinMap(), and pappso::cbor::psm::SageTsvHandler::recordLine().

◆ getProteinMap()

std::map< QString, pappso::cbor::psm::PsmProtein > & pappso::cbor::psm::PsmProteinMap::getProteinMap ( )

Definition at line 43 of file psmproteinmap.cpp.

{
  return m_proteinMap;
}

◆ insert()

std::pair< std::map< QString, pappso::cbor::psm::PsmProtein >::iterator, bool > pappso::cbor::psm::PsmProteinMap::insert ( const PsmProtein & psm_protein )

standard map insert of a PsmProtein (accession is the key)

Returns: standard C++ insert iterator on a map

Definition at line 50 of file psmproteinmap.cpp.

{
  return m_proteinMap.insert(
    std::pair<QString, PsmProtein>(psm_protein.protein_sp.get()->getAccession(), psm_protein));
}

References pappso::cbor::psm::PsmProtein::protein_sp.

Referenced by pappso::cbor::psm::MzIdentMlReader::finalDebrief(), pappso::cbor::psm::SageTsvHandler::parseProteins(), pappso::cbor::psm::CborScanMapBase::populateProteinMapUsingOldProteinMap(), and pappso::cbor::psm::SageTsvHandler::recordLine().

◆ merge()

void pappso::cbor::psm::PsmProteinMap::merge ( const PsmProteinMap & other_protein_map )

merge with other protein map

Definition at line 176 of file psmproteinmap.cpp.

{
  for(auto &it_prot : other_protein_map.m_proteinMap)
    {
      m_proteinMap.insert(std::pair<QString, PsmProtein>(it_prot.first, it_prot.second));
    }
}

References m_proteinMap.

◆ readMap()

void pappso::cbor::psm::PsmProteinMap::readMap ( CborStreamReader & reader )

reads the protein map from a cbor input stream

Parameters

reader the cbor intput stream

Definition at line 88 of file psmproteinmap.cpp.

{
  PsmProtein psm_protein;
  reader.enterContainer();
  while(!reader.lastError() && reader.hasNext())
    {
      bool is_ok;
 
      QString accession;
      is_ok = reader.decodeString(accession);
      qDebug() << accession;
      if(is_ok)
        {
          reader.enterContainer();
          pappso::Protein protein;
          protein.setAccession(accession);
          psm_protein.protein_sp    = std::make_shared<pappso::Protein>(protein);
          psm_protein.isContaminant = false;
          psm_protein.isTarget      = true;
          auto it = m_proteinMap.insert(std::pair<QString, PsmProtein>(accession, psm_protein));
 
          QString tag;
          while(!reader.lastError() && reader.hasNext())
            {
              is_ok = reader.decodeString(tag);
              qDebug() << tag;
              if(is_ok)
                {
                  if(tag == "description")
                    {
                      QString description;
                      is_ok = reader.decodeString(description);
                      qDebug() << description;
                      it.first->second.protein_sp.get()->setDescription(description);
                    }
                  else if(tag == "sequence")
                    {
                      QString sequence;
                      reader.decodeString(sequence);
                      it.first->second.protein_sp.get()->setSequence(sequence);
                    }
                  else if(tag == "target")
                    {
                      it.first->second.isTarget = reader.toBool();
                      reader.next();
                    }
                  else if(tag == "contaminant")
                    {
                      it.first->second.isContaminant = reader.toBool();
                      reader.next();
                    }
                  else if(tag == "eval")
                    {
                      reader.readCborMap(it.first->second.cborEval);
                    }
                }
            }
          reader.leaveContainer();
        }
      else
        {
          // no accession
        }
      // reader.next();
      // }
    }
  reader.leaveContainer();
}

References pappso::cbor::CborStreamReader::decodeString(), pappso::cbor::psm::PsmProtein::isContaminant, pappso::cbor::psm::PsmProtein::isTarget, pappso::cbor::psm::PsmProtein::protein_sp, pappso::cbor::CborStreamReader::readCborMap(), and pappso::Protein::setAccession().

Referenced by pappso::cbor::psm::PsmFileReaderBase::readProteinMap().

◆ reduce()

void pappso::cbor::psm::PsmProteinMap::reduce ( const QStringList & accession_list )

reduce to protein accessions listed in input

Definition at line 185 of file psmproteinmap.cpp.

{
  std::map<QString, PsmProtein> new_protein_map;
 
  for(const QString &accession : accession_list)
    {
      new_protein_map.insert(std::pair<QString, PsmProtein>(accession, getByAccession(accession)));
    }
  m_proteinMap = new_protein_map;
}

◆ size()

std::size_t pappso::cbor::psm::PsmProteinMap::size ( ) const

get protein map size

Definition at line 158 of file psmproteinmap.cpp.

{
  return m_proteinMap.size();
}

◆ writeMap()

void pappso::cbor::psm::PsmProteinMap::writeMap ( CborStreamWriter & writer ) const

writes the protein map in a cbor output stream this output a CborMap structure directly in the output stream

Parameters

writer the cbor output stream

Definition at line 57 of file psmproteinmap.cpp.

{
  // writer.append("protein_map");
  writer.startMap(m_proteinMap.size()); // protein map
  for(auto &protein_pair : m_proteinMap)
    {
      writer.append(protein_pair.first);
 
      qDebug() << protein_pair.first;
      writer.startMap(); // protein
      writer.append("description");
      writer.append(protein_pair.second.protein_sp.get()->getDescription());
      writer.append("sequence");
      writer.append(protein_pair.second.protein_sp.get()->getSequence());
      writer.append("target");
      writer.append(protein_pair.second.isTarget);
      writer.append("contaminant");
      writer.append(protein_pair.second.isContaminant);
 
      if(!protein_pair.second.cborEval.isEmpty())
        {
          writer.append("eval");
          writer.writeCborMap(protein_pair.second.cborEval);
        }
      writer.endMap(); // protein
    }
 
  writer.endMap(); // protein map
}

References pappso::cbor::CborStreamWriter::writeCborMap().

Referenced by pappso::cbor::psm::PsmFileScanProcessAndCopy::close(), pappso::cbor::psm::MzIdentMlReader::finalDebrief(), and pappso::cbor::psm::PsmFileScanProcessAndCopy::proteinMapReady().

Member Data Documentation

◆ m_proteinMap

std::map<QString, PsmProtein> pappso::cbor::psm::PsmProteinMap::m_proteinMap

private

Definition at line 110 of file psmproteinmap.h.

Referenced by merge().

The documentation for this class was generated from the following files:

pappsomspp/core/processing/cbor/psm/psmproteinmap.h
pappsomspp/core/processing/cbor/psm/psmproteinmap.cpp

Public Member Functions

Private Attributes